Geographic Difference Shaped Human Ocular Surface Metagenome of Young Han Chinese From Beijing, Wenzhou, and Guangzhou Cities/Experiment 1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Bulbar conjunctiva Ocular conjunctiva,Bulbar conjunctiva,bulbar conjunctiva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Health study participation health questionnaire participation,health survey participation,Health study participation,health study participation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Guangzhou healthy volunteers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bejing healthy volunteers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy nonsmokers from Bejing
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months prior to enrollment
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 4
Description: Figure 4: The characteristics of Guangzhou and Beijing conjunctival microbiome (A). The LDA effect size program was used to find the bacterial species which significantly distinguished Beijing (green) and Guangzhou (red) microbiomes (LDA score >3).
Abundance in Group 1: increased abundance in Bejing healthy volunteers
Revision editor(s): Mary Bearkland, Peace Sandy
Signature 2
Source: Figure 4
Description: Figure 4: The characteristics of Guangzhou and Beijing conjunctival microbiome (A). The LDA effect size program was used to find the bacterial species which significantly distinguished Beijing (green) and Guangzhou (red) microbiomes (LDA score >3).
Abundance in Group 1: decreased abundance in Bejing healthy volunteers
Revision editor(s): Mary Bearkland